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J C Thomas

Publications and source records attributed to J C Thomas.

At least 19 recordsLinked to original sources
PubMed2007

Inferring a population structure for Staphylococcus epidermidis from multilocus sequence typing data.

Despite its importance as a human pathogen, information on population structure and global epidemiology of Staphylococcus epidermidis is scarce and the relative importance of the mechanisms contributing to clonal diversification is unknown. In this study, we addressed these issues by analyzing a representative collection of S. epidermidis isolates from diverse geographic and clinical origins using multilocus sequence typing (MLST). Additionally, we characterized the mobile element (SCCmec) carrying the genetic determinant of methicillin resistance. The 217 S. epidermidis isolates from our collection were split by MLST into 74 types, suggesting a high level of genetic diversity. Analysis of MLST data using the eBURST algorithm revealed the existence of nine epidemic clonal lineages that were disseminated worldwide. One single clonal lineage (clonal complex 2) comprised 74% of the isolates, whereas the remaining isolates were clustered into 8 minor clonal lineages and 13 singletons. According to our evolutionary model, SCCmec was acquired at least 56 times by S. epidermidis. Although geographic dissemination of S. epidermidis strains and the value of the index of association between the alleles, 0.2898 (P < 0.05), support the clonality of S. epidermidis species, examination of the sequence changes at MLST loci during clonal diversification showed that recombination gives rise to new alleles approximately twice as frequently as point mutations. We suggest that S. epidermidis has a population with an epidemic structure, in which nine clones have emerged upon a recombining background and evolved quickly through frequent transfer of genetic mobile elements, including SCCmec.

Algorithms↗
PubMed2006

Continent catheterizable channels and the timing of their complications.

PURPOSE: We reviewed our experience with continent catheterizable channels with interest in the timing of conduit related complications. MATERIALS AND METHODS: A retrospective review was performed of the outcome of continent catheterizable channels in all patients between 1998 and 2003 who had undergone construction of an antegrade continence enema and/or a Mitrofanoff procedure using appendix, small bowel or continent cutaneous vesicostomy. We performed a total of 117 such stomas in 37 male and 41 female patients 2.5 to 20 years old (mean age 8.9). For the antegrade continence enema we used appendix in 92% of cases, an ileal Yang-Monti tube in 6% and a cecal tube in 2%. For the continent catheterizable channel we used appendix in 43% of cases, a Yang-Monti tube in 38% and continent cutaneous vesicostomy in 19%. RESULTS: Continence was achieved in 98% of patients. Followup was 6 to 71 months (mean 28.4). There were 27 channel related complications (23%). Stomal stenosis occurred in 7 antegrade continence enema procedures (14%) within 1 to 10 months (mean 6.2) and in 9 continent bladder channels (13%), including 5 continent cutaneous vesicostomies, within 1 to 24 months (mean 9.4) after surgery. False passages occurred in 5 antegrade continence enema procedures (10%) within 1 to 13 months (mean 3.6) and in 4 continent catheterizable channels (6%) within 1 to 13 months (mean 6.5) after surgery. Of patients with stomal stenosis 50% were treated with surgical revision, while the remainder was successfully treated with dilation. Most false passages were managed by catheter drainage alone. Reasons for revision were contained perforation, colovesical fistula and inability to catheterize. Patient noncompliance appeared to have a role in stomal stenosis. CONCLUSIONS: Continent catheterizable stomas help patients achieve bowel and bladder continence. Stomal incontinence after reconstruction is rare. In our experience most stoma related complications occurred in the first year after reconstruction. Experience with more patients and longer followup will help determine whether such problems continue to accumulate with time or whether continent stomas function well with time, particularly after the initial period of healing.

Adolescent↗
PubMed2005

First observation of 54Zn and its decay by two-proton emission.

The nucleus 54Zn has been observed for the first time in an experiment at the SISSI/LISE3 facility of GANIL in the quasifragmentation of a 58Ni beam at 74.5 MeV/nucleon in a (nat)Ni target. The fragments were analyzed by means of the ALPHA-LISE3 separator and implanted in a silicon-strip detector where correlations in space and time between implantation and subsequent decay events allowed us to generate almost background free decay spectra for about 25 different nuclei at the same time. Eight 54Zn implantation events were observed. From the correlated decay events, the half-life of 54Zn is determined to be 3.2(+1.8)(-0.8) ms. Seven of the eight implantations are followed by two-proton emission with a decay energy of 1.48(2) MeV. The decay energy and the partial half-life are compared to model predictions and allow for a test of these two-proton decay models.

Journal Article↗
PubMed2005

Management of the failed pyeloplasty: a contemporary review.

PURPOSE: We reviewed our experience with open dismembered pyeloplasty, with specific focus on the presentation and management of failed pyeloplasty in the pediatric population. MATERIALS AND METHODS: We performed a retrospective review of patients who had undergone open dismembered pyeloplasty between 1998 and 2003. All patients with less than 6 months of followup were excluded from analysis. The patients were followed postoperatively with serial ultrasounds, with renograms reserved for those patients with prolonged, persistent or worsening hydronephrosis, or recurrent symptoms during followup. RESULTS: A total of 105 pyeloplasties were performed in 103 patients (71 males and 32 females) 1 to 204 months old (mean 60), with an overall success rate of 93.3%. Followup ranged from 6 to 69 months (mean 23). The 7 patients with treatment failure were males 1 to 204 months old (mean 125), who presented most commonly with pain within 3 to 38 months (mean 13.1) after initial surgery. Subsequent ultrasound revealed worsening hydronephrosis, and renography in these patients showed a pattern consistent with obstruction. Five patients underwent initial balloon dilation, in which 1 was successful. In addition, 1 of these patients underwent an unsuccessful antegrade laser endopyelotomy. Six patients (86%) underwent open surgery, consisting of ureterocalicostomy in 3 and reoperative dismembered pyeloplasty in 3. Dense scarring was seen in all patients, 2 patients had a redundant pelvis causing kinking and 2 patients had unrecognized crossing vessels. Overall salvage rate was 100% with continued followup of 3 to 50 months (mean 18). CONCLUSIONS: Dismembered pyeloplasty was successful in the vast majority of patients. In our series failures occurred as late as 3 years postoperatively, although most presented within 12 months of followup. Excluding routine postoperative nuclear renography did not seem to affect our ability to identify these cases. Although anatomical features such as renal pelvic size may have a role, failure is most likely secondary to technical issues, including missed crossing vessels and dependency of the anastomosis. In this series failed pyeloplasties did not respond well to balloon dilation, likely due to scar formation. Our current practice is to manage failures by open surgery, although endoscopic management by an incision may be an option.

Adolescent↗
PubMed2001

Stromal testis tumors in children: a report from the prepubertal testis tumor registry.

PURPOSE: Stromal testis tumors are rare and generally exhibit a benign behavior in prepubertal patients. We reviewed the Prepubertal Testis Tumor Registry to elucidate further the behavior of these tumors. MATERIALS AND METHODS: Epidemiological and clinical information on stromal testis tumors was compiled and reviewed from the Prepubertal Testis Tumor Registry. In addition, original pathology reports were requested for all patients registered as having undifferentiated stromal tumors. RESULTS: There were 43 patients registered with stromal tumors. Of the 21 patients with unspecified stromal tumors pathology reports were obtained on 11. Eight patients had truly mixed or undifferentiated stromal tumors. Mean patient age at presentation was 38 months (Leydig cell 70, Sertoli cell 52.5, juvenile granulosa cell 1.5 and mixed/undifferentiated 41.2). No patient with a Leydig cell, Sertoli cell or juvenile granulosa cell tumor had metastases at presentation or metastatic disease during an average 24.6 months of followup. One undifferentiated tumor demonstrated malignant behavior by presenting with metastatic disease. Pathological examination revealed a poorly differentiated tumor with extension into the adjacent tunica and frequent mitotic figures. While other stromal tumors displayed mitotic figures, none showed local invasion. CONCLUSIONS: Stromal testis tumors are rare. Data from the Prepubertal Testis Tumor Registry confirms the benign behavior of most of these tumors. However, undifferentiated stromal tumors may exhibit metastatic behavior. A high index of suspicion is appropriate when there are a large number of mitotic figures, the tumor is poorly differentiated or when local invasion is present in the primary tumor. Metastatic evaluation and close followup are warranted for this select group of patients.

Adolescent↗
PubMed2001

Differential expression of antenna and core genes in Prochlorococcus PCC 9511 (Oxyphotobacteria) grown under a modulated light-dark cycle.

The continuous changes in incident solar light occurring during the day oblige oxyphototrophs, such as the marine prokaryote Prochlorococcus, to modulate the synthesis and degradation rates of their photosynthetic components finely. How this natural phenomenon influences the diel expression of photosynthetic genes has never been studied in this ecologically important oxyphotobacterium. Here, the high light-adapted strain Prochlorococcus sp. PCC 9511 was grown in large-volume continuous culture under a modulated 12 h-12 h light-dark cycle mimicking the conditions found in the upper layer of equatorial oceans. The pcbA gene encoding the major light-harvesting complex showed strong diel variations in transcript levels with two maxima, one before the onset of illumination and the other near the end of the photoperiod. In contrast, the mRNA level of psbA (encoding the reaction centre II subunit D1), the monocistronic transcript of psbD (encoding D2) and the dicistronic transcript of psbDC were all tightly correlated with light irradiance, with a minimum at night and a maximum at noon. The occurrence of a second peak during the dark period for the monocistronic transcript of psbC (encoding one of the PS II core Chl a antenna proteins) suggested the involvement of post-transcriptional regulation. Differential expression of the external antenna and core genes may constitute a mechanism of regulation of the antenna size to cope with the excess photon fluxes that Prochlorococcus cells experience in the upper layer of oceans around midday. The 5' ends of all transcripts were mapped, and a conserved motif, 5'-TTGATGA-3', was identified within the putative psbA and pcbA promoters.

Bacterial Proteins↗
PubMed2001

Nitrogen or sulfur starvation differentially affects phycobilisome degradation and expression of the nblA gene in Synechocystis strain PCC 6803.

Nitrogen (N) limitation in cyanobacteria is well documented: a reduced growth rate is observed, accompanied by a cessation of phycobiliprotein synthesis and an ordered degradation of phycobilisomes (PBS). This leads to a dramatic bleaching phenomenon known as chlorosis. In Synechococcus strain PCC 7942, bleaching due to PBS degradation is also observed under sulfur (S) or phosphorus (P) limitation, and all three are under the control of the nblA gene product, a 59-amino-acid polypeptide which is overexpressed under N, S, and P starvation (J. L. Collier, and A. R. Grossman, EMBO J. 13:1039-1047, 1994). Cyanobase sequence data for Synechocystis strain PCC 6803 indicate the presence of two tandem open reading frames (sll0452 and sll0453) homologous to nblA. We cloned the two genes, identified a unique 5' mRNA end suggestive of a single transcription start site, and studied nblA expression under conditions of N or S starvation by Northern hybridization: transcripts were detected only under N starvation (no signal is detected in replete medium or with S starvation), whether nblA1 or nblA2 was used as a probe. Mutations in nblA1 and nblA2 were constructed by insertion of a kanamycin cassette; both mutations were nonbleaching under N starvation. Synechocystis strain PCC 6803 does not bleach under S starvation, consistent with the absence of nblA induction in these conditions. These results were confirmed by analysis of the PBS components: sequential degradation of phycocyanin and associated linkers was observed only under conditions of N starvation. This indicates differences between Synechocystis strain PCC 6803 and Synechococcus strain PCC 7942 in their regulatory and signaling pathways leading to N- and S-starved phenotypes.

Bacterial Proteins↗
PubMed2001

When is sex safe? Insiders' views on sexually transmitted disease prevention and treatment.

STD prevention programs promote practices and messages that are presumed to fit with most conditions of U.S. communities. Yet, the social and cultural contexts for low-income ethnic communities may frame STD prevention differently, so that people calculate their risk and take actions based on what they have learned through their own observations and life experiences. To understand how people at high risk for STDs make decisions and take actions to protect themselves from these diseases, the authors conducted 38 ethnographic interviews with individuals living in arural community in the South. Practices they reported include selecting "safe" partners on the basis of appearance, familiarity, or church attendance; washing before and after sex to prevent infection; self-treatment with antibiotics obtained without a prescription; and visiting the clinic frequently for checkups for asymptomatic infections. The authors compare and contrast their worldview with the public health concepts of primary and secondary STD prevention.

Adolescent↗
PubMed2001

Thoracoscopic transdiaphragmatic adrenalectomy: the initial experience.

PURPOSE: We introduce the technique of thoracoscopic transdiaphragmatic adrenalectomy. MATERIALS AND METHODS: Initially in 4 human cadavers bilateral thoracoscopic nephrectomy was performed to develop the technique of diaphragmatic incision, retroperitoneal control of renal artery and vein, circumferential mobilization of the kidney and adrenal gland, and suture repair of the diaphragm. Subsequently, 3 select patients underwent thoracoscopic transdiaphragmatic adrenalectomy (2 right side and 1 left side). All 3 patients had significant prior abdominal scarring after either partial or total radical nephrectomy, thereby precluding efficient transabdominal laparoscopic access to the adrenal gland. After double lumen endotracheal intubation, a 4 port transthoracic approach without pneumo-insufflation was performed with the patient in the prone position. The diaphragm was incised under real-time laparoscopic ultrasound guidance. The adrenal gland was visualized high in the retroperitoneum, the vasculature controlled, and the specimen entrapped and extracted intact through a thoracic port site. The diaphragm was suture repaired with freehand laparoscopic suturing and intracorporeal knot tying. A chest tube was inserted in the initial 2 patients. RESULTS: There were no intraoperative or postoperative complications. Operating time was 4.5, 6.5 and 2.5 hours, and blood loss was 150, 500 and 50 cc, respectively. Mean narcotic analgesic requirement was 27 mg. morphine sulfate equivalent. Hospital stay was 2 days for all 3 patients. Pathology revealed metastatic renal cell carcinoma in 2 patients and myelolipoma in 1. CONCLUSIONS: In select patients with significant concomitant intraperitoneal and retroperitoneal scarring from prior major abdominal or renal surgery laparoscopic adrenalectomy can be safely performed with the transthoracic transdiaphragmatic approach. We present our initial experience.

Adrenal Gland Neoplasms↗
PubMed2001

An improved method for evaluating hardwood animal bedding products.

Technological improvements have led to the development of higher quality hardwood bedding products with lower dust content. Nevertheless, testing procedures used to evaluate the quality of laboratory animal bedding products have not kept pace, resulting in the continued use of flawed and outdated test methods. The present study was conducted to develop an improved method for evaluating the quality of hardwood animal bedding products.

Animals↗
PubMed2000

Kinetics of photoacclimation in response to a shift to high light of the red alga Rhodella violacea adapted to low irradiance.

The unicellular rhodophyte Rhodella violacea can adapt to a wide range of irradiances. To create a light stress, cells acclimated to low light were transferred to higher irradiance and the kinetics of various changes produced by the light shift were analyzed. The proton gradient generated by excess light led to a non-photochemical quenching of the chlorophyll fluorescence and some photoinhibition of photosystem II centers was also produced by the light stress. After the shift to higher irradiance, the mRNA levels of three chloroplast genes that encode phycoerythrin and phycocyanin apoproteins and heme oxygenase (the first enzyme specific to the bilin synthesis) were negatively regulated. A change in the amount of thylakoids and in the total pigment content of the cells occurred during light acclimation after a light stress. The change in the size of the phycobilisome was limited to dissapearance of the terminal phycoerythrin hexamers in some of the rods. The ability of R. violacea to photoacclimate depends both on large changes in thylakoid number and pigment content and on smaller changes in the antenna size of photosystem II.

Acclimatization↗
PubMed2000

Factors associated with periodontitis in an HIV-infected southeast USA study.

OBJECTIVES: To determine the relationship of immunosuppression with measures of probing pocket depth (PPD), recession (REC), and clinical attachment level (CAL) in an HIV-infected population from North Carolina (NC), a state in the southeastern United States (USA). DESIGN: Cross-sectional study of HIV-infected adults (n = 326) treated at the University of North Carolina Hospitals. Clinical medical record review and sociodemographic interview data were collected. Median age of study participants was 37 years (range 19-67). Males comprised 78% and Blacks 60%. Analyses were limited to those who were dentate (n = 316). MAIN OUTCOME MEASURES: Main outcomes were cases vs non-cases of notable PPD, REC, and CAL. Immunosuppression measured by CD4+ cell count microL was the exposure of interest. RESULTS: Defined cases of PPD (n = 148) were 2.6 (95% CI = 1.3, 5.3) times less likely to occur at CD4+ cells < 200 than non-cases, whereas, cases of REC (n = 94) were 2.8 (95% CI = 1.2, 6.6) times more likely to occur at that level of severe immunosuppression, controlling for confounders. CONCLUSION: Sub-groups of persons with HIV experience a high burden of periodontitis where notable severity and extent of PPD, CAL, and REC were clearly evident at different stages of immunosuppression.

AIDS-Related Opportunistic Infections↗
PubMed2000

Monitoring by laser-flow-cytometry of the polycyclic aromatic hydrocarbon-degrading Sphingomonas sp. strain 107 during biotreatment of a contaminated soil.

A flow cytometric method (FCM) was used to detect and accurately enumerate a polycyclic aromatic hydrocarbon-degrading bacterial strain, Sphingomonas sp. 107, inoculated into a soil sample artificially contaminated with pyrene. To compare the FCM method with colony forming unit (CFU) assays, a rifampicin-resistant Sphingomonas sp. 107 was obtained which could be distinguished from the indigenous microflora, since there was no organism resistant to rifampicin in the soil that could transform indole to indigo (naphthalene dioxygenase activity). By combining light-scattering profiles (i.e., morphological properties), ethidium bromide influx (i.e., cell wall permeability), and fluorescence in situ hybridization against the 16S rRNA (i.e., detection specificity), we could enumerate the bacterial population of interest from the indigenous microflora and soil debris during the biotreatment. The FCM technique revealed that the number of inoculated Sphingomonas cells decreased gradually for 15 days of incubation before reaching a steady level of 7 to 12 x 10(5) cells.g-1 of soil. Similar values were obtained with the CFU assay. During this period, pyrene concentration decreased from 632 to 26 mg.kg-1 of dry soil. The FCM detection was improved by adding blocking reagent to the hybridization buffer to minimize the non-specific attachment of the fluorescent probe to soil particles. Combined with the improvements in probe technology, FCM detection was shown to be a good alternative to the conventional culture methods for the analysis of bacterial populations in environmental samples. This technique could be potentially useful for the detection of microorganisms that grow poorly in culture.

Biodegradation, Environmental↗
PubMed2000

Evaluation and lessons learned from a lay health advisor programme to prevent sexually transmitted diseases.

We implemented a lay health advisor (LHA) intervention to decrease rates of sexually transmitted disease (STD) among rural low income African-Americans. Twenty-one women identified by their peers as natural helpers were trained as LHAs to disseminate information, change attitudes, and improve skills among their social networks in the neighbourhoods with the highest STD rates. The behaviours they targeted involved care-seeking and condom use. The outcome evaluation included cross-sectional household surveys conducted before the intervention and after 18 months of activity. The proportion seeking prompt care for an STD increased 60%; those seeking screening for infection after suspecting exposure increased 25%. Consistent condom use with main partners increased by 23%. An LHA intervention in this population appears efficacious for improving STD-related care seeking behaviours but the effect on condom use with main partners is less clear.

Adult↗
PubMed2000

Frequent re-infection in a community with hyperendemic gonorrhoea and chlamydia: appropriate clinical actions.

In a cohort of 1200 individuals experiencing an index infection of gonorrhoea or chlamydia in a rural North Carolina county, we studied the risk factors for re-infection within 16 months. The occurrence of asymptomatic re-infection was estimated from a sample of controls. Re-infection with either of the two STDs occurred in one-quarter (24%) of the study participants and 22% of the controls. The factors associated with re-infection were age less than 25 years, African-American race, male sex, and infection prior to the index infection. The behavioural and attitudinal variables tested were not associated with re-infection. The patterns of re-infection in this study do not provide guidance for targeting resources toward a subgroup of the clinic population. Structuring clinical services to make them more available and acceptable to all potential clinic clients can contribute to decreasing the duration of infections. Lowering the community prevalence in this way will then decrease the likelihood of re-infection rates.

Adolescent↗
PubMed2000

Use of fenofibrate in the management of protease inhibitor-associated lipid abnormalities.

Human immunodeficiency virus (HIV) protease inhibitors are associated with several metabolic abnormalities including hypercholesterolemia and hypertriglyceridemia. Fenofibrate is a new lipid-lowering agent for adults with very high triglyceride levels that was administered to two HIV-positive patients who were taking protease inhibitors and developed hypertriglyceridemia. Starting dosages were 134 and 201 mg/day, and were increased to 268 mg/day in both patients. Triglyceride levels decreased from 1450 to 337 mg/dl (76.8%) and from 1985 to 322 mg/dl (83.8%), respectively, after 10 months of therapy. High-density lipoprotein levels increased in both patients.

Adult↗